i've seen this behaviour too, but only once or twice
at this resolution sigma(free R) is roughly 0.5-0.6 so the
differences may or may not be significant
i would check the resulting models to see if they differ
in a few areas (in that case the data might be telling
you something, e.g. that the harmonic or ncs restraints
should be loosened or released in those areas)
also, the difference between r and rfree increases as WA increases;
depending on how complete your model is this may not be what you
want
--gerard